Magnesium in PDB 6nmk: Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin

Protein crystallography data

The structure of Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin, PDB code: 6nmk was solved by M.J.Cuneo, B.Selvaraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.07 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.000, 97.710, 101.970, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.1

Other elements in 6nmk:

The structure of Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin (pdb code 6nmk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin, PDB code: 6nmk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6nmk

Go back to Magnesium Binding Sites List in 6nmk
Magnesium binding site 1 out of 2 in the Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:46.0
occ:1.00
OE1 A:GLU145 2.1 48.3 1.0
O4 B:NMY302 2.6 40.0 1.0
O B:HOH463 2.6 37.6 1.0
CD A:GLU145 3.0 52.0 1.0
N9 B:NMY302 3.0 31.8 1.0
C5 B:NMY302 3.0 41.9 1.0
C4 B:NMY302 3.1 48.5 1.0
O B:HOH416 3.2 42.1 1.0
OE2 A:GLU145 3.2 56.1 1.0
C3 B:NMY302 3.5 45.5 1.0
OE1 B:GLU76 3.5 30.5 1.0
O B:HOH533 3.5 51.1 1.0
C6 B:NMY302 3.7 51.1 1.0
NZ B:LYS74 3.7 42.0 1.0
O1 B:NMY302 4.0 39.2 1.0
OE2 B:GLU67 4.0 28.1 1.0
OE2 B:GLU52 4.0 43.2 1.0
N6 B:NMY302 4.2 45.7 1.0
O5 B:NMY302 4.2 42.1 1.0
C9 B:NMY302 4.3 32.9 1.0
CG A:GLU145 4.3 38.3 1.0
O3 B:NMY302 4.3 38.5 1.0
C1 B:NMY302 4.5 45.7 1.0
C2 B:NMY302 4.5 42.1 1.0
O A:GLU141 4.5 27.8 1.0
C10 B:NMY302 4.6 39.0 1.0
CD B:GLU76 4.7 30.2 1.0
CE B:LYS74 4.8 33.8 1.0
O B:HOH499 4.9 23.3 1.0

Magnesium binding site 2 out of 2 in 6nmk

Go back to Magnesium Binding Sites List in 6nmk
Magnesium binding site 2 out of 2 in the Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:45.2
occ:1.00
OE2 B:GLU145 2.3 44.1 1.0
O4 A:NMY301 2.5 34.0 1.0
C5 A:NMY301 2.7 48.4 1.0
N9 A:NMY301 2.8 34.5 1.0
OE1 B:GLU145 2.9 52.0 1.0
CD B:GLU145 2.9 48.9 1.0
C4 A:NMY301 3.0 39.2 1.0
O A:HOH459 3.0 31.6 1.0
O A:HOH500 3.3 43.4 1.0
C3 A:NMY301 3.3 42.8 1.0
OE1 A:GLU76 3.5 31.7 1.0
O A:HOH447 3.6 44.0 1.0
C6 A:NMY301 3.6 49.8 1.0
NZ A:LYS74 3.8 31.3 1.0
O1 A:NMY301 3.8 33.6 1.0
O5 A:NMY301 3.9 37.1 1.0
C9 A:NMY301 4.1 33.5 1.0
C1 A:NMY301 4.2 37.7 1.0
OE1 A:GLU52 4.2 37.7 1.0
OE1 A:GLU67 4.3 22.3 1.0
N6 A:NMY301 4.3 52.0 1.0
O3 A:NMY301 4.3 34.1 1.0
C2 A:NMY301 4.3 34.9 1.0
C10 A:NMY301 4.3 37.4 1.0
CG B:GLU145 4.4 35.0 1.0
O B:GLU141 4.5 27.3 1.0
CD A:GLU76 4.7 22.7 1.0
O B:HOH405 4.9 45.0 1.0

Reference:

P.Kumar, E.H.Serpersu, M.J.Cuneo. Catch and Release: A Novel Variation of the Archetypal Nucleotidyl Transfer Reaction To Be Published.
Page generated: Mon Dec 14 23:40:50 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy